Thank you, sir, for your reply .
I want to do capping of C-terminal with NME and N-terminal with ACE. But In case Of NME it works fine (according to the manual) but in the case of ACE, there is problem.2rd6-new.pdb is the main PDB . After following the steps I have got 2rd6-leap-1.pdb.
1) Get the PDB
2)Add hydrogens
3)Load into xleap
4)xleap will add OXT terms to ends of chains
5) In adding NME, just remove the OXT oxygen and in that place, put the N atom of NME (if adding a new atom, atom number is zero. Keep the residue
number as it is)
6) To add ACE groups, from each N terminal, remove two hydrogens bound to N eg:- H1,H2 or H3 Then put the ACE carbon atom
7) Now load the file into xleap
There will be some messages about splitting residues because ACE and the following amino acids as well as NME and the following amino acids both have the same residue numbers
8)Some unknown hydrogens will be added into the residue after the ACE.
Please help me out .
Thanks
Saikat
On Thursday, 15 June 2017 7:54 PM, David Case <david.case.rutgers.edu> wrote:
On Thu, Jun 15, 2017, Saikat Pal wrote:
> Thank you sir for your kind response . This is my main pdb
> (2rd6-new.pdb) and after capping pdb (2rd6-leap-1.pdb).I have attached
> these pdbsin this mail.Thanks and regards,saikat
Your 2rd6-leap-1.pdb file is quite odd. It has two chains: the first chain
just has a single lysine residue. A single amino-acid peptide is non-standard
for Amber, since otherwise it doesn't know whether to treat the residue
as a N-terminal or C-terminal residue.
Of equal or greater concern, the position of LYS 1 is almost the same
as LYS 3. I don't really understand how you came up with this model, but
something seems to have gone quite awry. What happens if you just remove
LYS 1?
....dac
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Received on Thu Jun 15 2017 - 08:00:02 PDT
